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Cadmium in PDB 7d1p: Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site

Enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site

All present enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site, PDB code: 7d1p was solved by K.-F.Huang, J.-S.Huang, M.-L.Wu, W.-L.Hsieh, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.27 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.516, 73.766, 84.421, 90, 90, 90
R / Rfree (%) 18.3 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site (pdb code 7d1p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site, PDB code: 7d1p:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 1 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:30.2
occ:1.00
 OE1 A:GLU184 2.0 29.3 1.0
NE2 A:HIS322 2.2 33.2 1.0
O1 A:BCT410 2.3 40.2 1.0
OD2 A:ASP144 2.3 25.9 1.0
CD A:GLU184 2.8 27.8 1.0
OE2 A:GLU184 2.8 29.5 1.0
CD2 A:HIS322 3.1 31.3 1.0
CG A:ASP144 3.2 27.7 1.0
C A:BCT410 3.2 46.5 1.0
CE1 A:HIS322 3.3 29.4 1.0
CD A:CD402 3.3 41.6 1.0
OD1 A:ASP144 3.4 32.4 1.0
O2 A:BCT410 3.6 48.4 1.0
NE1 A:TRP321 3.7 36.0 1.0
O3 A:BCT410 4.2 50.0 1.0
O A:HOH522 4.2 21.0 1.0
CG A:GLU184 4.2 28.2 1.0
CG A:HIS322 4.3 29.9 1.0
OE1 A:GLU183 4.3 44.4 1.0
ND1 A:HIS322 4.3 28.8 1.0
CD1 A:TRP321 4.5 33.5 1.0
CB A:ASP144 4.6 29.1 1.0
CE2 A:TRP321 4.6 37.8 1.0
CD2 A:LEU239 4.7 24.9 1.0
O A:HOH520 4.8 24.7 1.0
CZ2 A:TRP321 4.9 41.2 1.0

Cadmium binding site 2 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 2 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:41.6
occ:1.00
 NE2 A:HIS128 2.4 22.9 1.0
OD1 A:ASP144 2.5 32.4 1.0
OD1 A:ASP238 2.6 40.2 1.0
O1 A:BCT410 2.6 40.2 1.0
OE1 A:GLU183 2.9 44.4 1.0
OE2 A:GLU183 2.9 47.3 1.0
C A:BCT410 3.1 46.5 1.0
O2 A:BCT410 3.2 48.4 1.0
CD A:GLU183 3.3 40.0 1.0
CG A:ASP238 3.3 41.7 1.0
CE1 A:HIS128 3.3 23.5 1.0
CG A:ASP144 3.3 27.7 1.0
CD2 A:HIS128 3.3 22.8 1.0
CD A:CD401 3.3 30.2 1.0
OE1 A:GLU184 3.4 29.3 1.0
OD2 A:ASP238 3.4 56.1 1.0
OD2 A:ASP144 3.6 25.9 1.0
OG A:SER145 3.8 29.6 1.0
CD A:CD403 4.0 73.7 1.0
CD2 A:LEU239 4.1 24.9 1.0
CD A:GLU184 4.1 27.8 1.0
O3 A:BCT410 4.2 50.0 1.0
ND1 A:HIS128 4.4 22.8 1.0
CG A:HIS128 4.4 22.6 1.0
CB A:ASP144 4.5 29.1 1.0
CB A:ASP238 4.6 33.6 1.0
OE2 A:GLU184 4.7 29.5 1.0
CA A:ASP144 4.7 27.8 1.0
CG A:GLU183 4.8 34.2 1.0
C A:ASP144 4.8 27.3 1.0
CG A:LEU239 4.9 25.0 1.0
O A:HOH522 4.9 21.0 1.0
CG A:GLU184 4.9 28.2 1.0
CB A:SER145 5.0 28.2 1.0

Cadmium binding site 3 out of 9 in 7d1p

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Cadmium binding site 3 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:73.7
occ:1.00
 OD2 A:ASP297 2.4 51.9 1.0
OE2 A:GLU183 2.5 47.3 1.0
OD1 A:ASP297 2.5 42.0 1.0
OD2 A:ASP238 2.5 56.1 1.0
O A:HOH505 2.8 52.3 1.0
CG A:ASP297 2.8 44.8 1.0
CG A:ASP238 3.1 41.7 1.0
CD A:GLU183 3.5 40.0 1.0
CB A:ASP238 3.6 33.6 1.0
CD2 A:HIS128 3.8 22.8 1.0
OD2 A:ASP298 3.9 54.7 1.0
OD1 A:ASP238 3.9 40.2 1.0
CD A:CD402 4.0 41.6 1.0
CG A:GLU183 4.0 34.2 1.0
CB A:ASP297 4.2 48.2 1.0
O2 A:BCT410 4.3 48.4 1.0
NE2 A:HIS128 4.3 22.9 1.0
CD1 A:LEU236 4.4 37.7 1.0
OE1 A:GLU183 4.4 44.4 1.0
CG A:ASP298 4.5 54.0 1.0
NE2 A:HIS311 4.6 32.2 1.0
CD2 A:LEU236 4.6 38.0 1.0
N A:ASP298 4.6 54.2 1.0
CG A:LEU236 4.6 34.7 1.0
CB A:ASP298 4.8 52.2 1.0
C A:BCT410 4.8 46.5 1.0
CG A:HIS128 4.9 22.6 1.0

Cadmium binding site 4 out of 9 in 7d1p

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Cadmium binding site 4 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:35.6
occ:1.00
 O A:HOH540 2.3 40.3 1.0
NE2 A:HIS40 2.5 30.8 1.0
OD2 A:ASP41 2.5 27.2 1.0
OD1 A:ASP41 2.6 27.9 1.0
CG A:ASP41 2.9 26.9 1.0
CD2 A:HIS40 3.2 30.1 1.0
CE1 A:HIS40 3.4 33.1 1.0
NZ A:LYS162 4.1 46.5 1.0
CB A:ASP41 4.3 26.0 1.0
CG A:HIS40 4.3 29.6 1.0
ND1 A:HIS40 4.4 31.1 1.0
CA A:ASP41 4.8 27.1 1.0
N A:ASP41 4.9 26.6 1.0
OXT A:LEU353 5.0 48.6 1.0

Cadmium binding site 5 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 5 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:68.1
occ:1.00
 OE2 A:GLU50 2.8 57.2 1.0
OE1 A:GLU50 2.9 57.2 1.0
CD A:GLU50 3.2 51.9 1.0
NE A:ARG53 4.3 39.7 1.0
CG A:GLU50 4.6 46.9 1.0
CD A:ARG53 4.8 37.0 1.0
CZ A:ARG53 5.0 42.0 1.0
NH2 A:ARG53 5.0 41.1 1.0

Cadmium binding site 6 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 6 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:30.1
occ:1.00
 O A:HOH538 2.0 16.1 1.0
OE2 A:GLU51 2.2 37.6 1.0
OE1 A:GLU51 2.5 38.1 1.0
CD A:GLU51 2.7 35.9 1.0
CG A:GLU51 4.2 34.3 1.0
O A:HOH573 4.5 32.3 1.0
CB A:GLU51 4.9 32.5 1.0

Cadmium binding site 7 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 7 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:78.1
occ:1.00
 OD1 A:ASP89 2.7 41.8 1.0
O A:HOH594 2.9 35.0 1.0
OD2 A:ASP89 3.3 48.4 1.0
CG A:ASP89 3.3 39.3 1.0
CB A:ASP89 4.7 32.1 1.0
O A:ASP87 4.9 34.3 1.0

Cadmium binding site 8 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 8 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd408

b:36.0
occ:1.00
 OD1 A:ASN165 2.4 27.0 1.0
CG A:ASN165 3.4 24.6 1.0
ND2 A:ASN165 3.8 25.5 1.0
OG1 A:THR168 4.0 32.5 1.0
CB A:ASN165 4.6 26.0 1.0
O A:ASN165 4.6 27.5 1.0
CA A:ASN165 4.9 25.5 1.0

Cadmium binding site 9 out of 9 in 7d1p

Go back to Cadmium Binding Sites List in 7d1p
Cadmium binding site 9 out of 9 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cd Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd409

b:37.0
occ:1.00
 NE2 A:HIS333 2.3 36.8 1.0
O A:HOH510 2.3 22.9 1.0
OE1 A:GLU328 2.4 37.1 1.0
O A:HOH567 2.5 25.4 1.0
O A:HOH519 2.5 16.9 1.0
O A:HOH589 2.7 34.7 1.0
CE1 A:HIS333 3.0 35.1 1.0
CD A:GLU328 3.2 39.9 1.0
O A:HOH575 3.2 43.3 1.0
OE2 A:GLU328 3.3 37.4 1.0
CD2 A:HIS333 3.4 35.9 1.0
O A:GLU328 4.0 34.7 1.0
O A:HOH564 4.2 40.4 1.0
ND1 A:HIS333 4.2 36.4 1.0
CG A:HIS333 4.5 34.6 1.0
O A:LEU331 4.6 33.0 1.0
CG A:GLU328 4.6 40.0 1.0
O A:HOH563 4.8 41.8 1.0
C A:GLU328 4.9 34.6 1.0

Reference:

K.F.Huang, J.S.Huang, M.L.Wu, W.L.Hsieh, K.C.Hsu, H.L.Hsu, T.P.Ko, A.H-J Wang. A Unique Carboxylic-Acid Hydrogen-Bond Network (Cahbn) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. J.Mol.Biol. 66960 2021.
ISSN: ESSN 1089-8638
PubMed: 33774034
DOI: 10.1016/J.JMB.2021.166960
Page generated: Fri Jul 19 19:54:56 2024

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